similar to: stepwise variable selection method wanted

Note that cophenetic.default (which works on the output of hclust(dist(X))) uses the row names of X as labels. as.dendrogram.hclust does not retain those row names so cophenetic.dendrogram cannot use them (so it orders them based on the topology of the dendrogram). Bill Dunlap TIBCO Software wdunlap tibco.com On Thu, Apr 21, 2016 at 7:59 AM, William Dunlap <wdunlap at tibco.com> wrote:

Hello, I have been using the "cophenetic" function for objects of class "dendrogram" and I have realised that it gives different results when it is used with objects of class "hclust". For instance, running the first example in the help file of the "cophenetic" function, d1 <- dist(USArrests) hc <- hclust(d1, "ave") d2 <-

I think the results differ only in the order of the labels. The following function puts the labels in a standard order and then the results are the same: canonicalize.dist <- function (distObject) { o <- order(labels(distObject)) as.matrix(distObject)[o, o, drop = FALSE] } identical(canonicalize.dist(d2), canonicalize.dist(d3)) [1] TRUE Bill Dunlap TIBCO Software

Hello, I've been trying to figure out how to access the individual elements from an object of class phylo. I am reading in 201 trees created by paup as below. > read.nexus("A_30knj_200t.txt", tree.names= NULL) -> anj30 > anj30[1] $tree1 $edge [,1] [,2] [1,] "-1" "-2" [2,] "-2" "-3" [3,] "-3" "1"

Hello, I analyse some free-sorting data so I use hierarchical clustering. I want to compare my proximity matrix with the tree representation to evalute the fitting. (stress, cophenetic correlation (pearson's correlation)...) "The cophenetic similarity of two objects a and b is defined as the similarity level at wich objects a and b become members of the same cluster during the course of

Hi, How could we print the frequency table (produced by "table") to an Excel file? Is there an easy way to do so? Thanks, Miao > df <- data.frame(x = 1:3, y = 3:1, z = letters[1:3]) > table(df[,c("y","z")]) z y a b c 1 0 0 1 2 0 1 0 3 1 0 0 > test<-table(df[,c("y","z")]) > as.data.frame(test) y z Freq 1 1 a

Dear all, I have to handle a large matrix (1000 x 10001) where in the last column i have a value that all the preceding values in the same row has to be compared to. I have made the following code : # generate a (1000 x 10001) matrix, testm # generate statistics matrix 1000 x 4: qnt <- c(0.01, 0.05) cmp_fun <- function(x) { LAST <- length(x) smpls <- x[1:(LAST-1)] real

Hi jpm miao, You can get CSV files that can be imported into Excel like this: library(prettyR) sink("excel_table1.csv") delim.table(table(df[,c("y","z")])) sink() sink("excel_table2.csv") delim.table(as.data.frame(table(df[,c("y","z")])),label="") sink() sink("excel_table3.csv")

Dear All, I wrote a function for cluster analysis to compute cophenetic correlations between dissimilarity matrices (using the VEGAN library) and cluster analyses of every possible clustering algorithm (SEE ATTACHED) http://old.nabble.com/file/p26288610/cor.coef.R cor.coef.R . As it is now, it is extremely long, and for the future I was hoping to find a more efficient way of doing this sort of

Of interest to some on the list. Anyone familiar enough with Java to know how we go about detecting/using/incorporating an external Jorbis build into the Cortado jar ? Or are we supposed to download sources into our tree and build the whole ? ---------- Forwarded message ---------- From: Hans de Goede <hdegoede at redhat.com> Date: Thu, 04 Nov 2010 15:31:31 +0100 Subject: Merging jorbis

I did not post this question to the ecology list, even though it is about an analysis using Vegan, since my question is based more on basic data manipulation in R. I think this is a fairly simple question but for the life of me I cannot find a reference for in the archives. I have an analysis using a matrix in which I needed to strip the ID variable off the input data to run the analysis. Now I

Hi everyone, I have a rollapply statement that applies a function, in steps, over a data matrix as follows: #Code start testm<-rollapply(mat, 100, by=100, min, na.rm=F) #Code end This moves down matrix 'mat' and calculates the minimum value over a 100 row range, every 100 rows (i.e. no overlaps). NAs are not removed. I want to modify this statement somehow so that the rollapply()

I know that within sum of squares, DB, sillhouette and cophenetic are indicators of clustering quality, but what indicators I need to observe when I choose attributes for kmeans? -- View this message in context: http://r.789695.n4.nabble.com/Feature-selection-for-kmeans-tp4657830.html Sent from the R help mailing list archive at Nabble.com.

Is there a function available in R that implements Mojena's Upper Tail Rule or that draws a Mojena plot? I would also like to find a function that implements Duda and Hart's stopping rule. Finally with function cophenet how can I achieve a straightforward Cophenet correlation coefficient (i.e. one number for example 0.876) that gives the agreement between the structure of the

This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_000_01C35A53.75780090 Content-Type: text/plain; charset="iso-8859-1" Anyone have a clue why hclust() and agnes() produce different results in the example below when both use method="average"?? I'm not able to reproduce

Hello, I am trying to preform a comparative analysis using the partial mantel method. However, i am having trouble creating compatible matrices. I can create matrices from my numerical data using the 'distance(x, method)' function from ecodist, but the row/column names are out put as numbers. While when i create a phyo-distance matrix using 'cophenetic(x)' from APE, the row/column

Hello, I'm trying to take the correlation of two distance matrices and get the r2 value ex) Ndisc PS1 Ntet Nsito NcB NcA PS3 NcC NiB NiA PS1 0.08945 Ntet 0.08601 0.02020 Nsito 0.09361 0.02780 0.02260

thank you i have succed to install lingoes with your advice, but it doesn't work properly, because it doesn't capture words on screen when i active the mode. It works fine only on the lingoes window

Hello. I've got a problem logging in to a Sparc Solaris 10 machine with public key authentication. I searched, and found a similar problem report at <http://thread.gmane.org/gmane.network.openssh.devel/12694>. For that guy, the problem had to do with LDAP. My user accounts are also stored in LDAP, an OpenLDAP server, to be exact. That server runs on the same machine as the machine

Greeting- I have a mixed network of ms-windows, macintosh and freebsd systems. I am setting up a FreeBSD 9.0 system as a PDC using samba. I can from a FreeBSD box attach to the SMB server as a user that is defined on the Samba Server. [wynkoop at dt0 ~]$ smbclient -L hp1 Enter wynkoop's password: Domain=[HARAPARTNERS] OS=[Unix] Server=[Samba 3.6.4] Sharename Type